Contacts of the strand formed by residues 3 - 7 (chain H) in PDB entry 5M32
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 3 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H THR 5.6 0.4 - - - -
2H THR* 1.3 79.1 - - - +
4H ALA* 1.3 70.4 + - - +
15H GLY 3.1 20.9 - - - +
16H ALA* 3.8 14.8 - - + -
33H LYS* 4.4 2.9 - - + +
44H CYS* 2.8 43.7 - - + -
45H GLY 3.4 22.4 - - - +
46H ALA* 5.2 3.4 - - + -
98H LEU* 6.1 0.2 - - - -
99H VAL* 4.8 6.7 - - + +
126H THR* 3.6 17.4 - - - +
127H MET* 3.2 47.8 + - + +
131H SER 5.3 0.2 + - - -
134H ALA* 4.8 0.2 - - - +
159H ILE* 3.6 4.1 - - - +
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Residues in contact with ALA 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 1.3 85.3 - - - +
5H GLY* 1.3 59.8 + - - +
14H LEU* 3.4 6.0 - - - +
15H GLY 3.0 31.2 + - - +
44H CYS* 4.6 0.3 - - - -
99H VAL* 5.1 2.5 - - - -
125H VAL* 3.3 17.5 - - - +
126H THR* 3.9 2.7 - - + -
134H ALA* 5.2 0.7 - - + -
138H PHE* 3.8 22.9 - - + -
155H VAL* 4.6 5.2 - - + -
158H ALA* 4.7 3.8 - - + -
159H ILE* 3.8 17.0 - - + -
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Residues in contact with GLY 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ALA* 1.3 78.2 - - - +
6H VAL* 1.3 64.2 + - - +
13H VAL 3.1 13.5 - - - -
14H LEU* 4.0 13.0 - - - -
110H LEU* 3.7 12.2 - - - +
124H TYR* 3.3 5.7 - - - +
125H VAL* 3.3 31.2 + - - +
138H PHE* 4.6 1.2 - - - -
155H VAL* 4.9 1.5 - - - +
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Residues in contact with VAL 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H GLY* 1.3 77.6 - - - +
7H VAL* 1.3 75.6 + - - +
8H TYR* 4.0 2.8 + - - -
12H ILE* 3.3 1.6 - - - -
13H VAL* 2.9 31.6 + - + +
110H LEU* 3.9 4.2 - - - +
123H PRO 3.7 2.7 - - - -
124H TYR* 4.1 7.4 - - + -
138H PHE* 3.6 35.4 - - + -
142H PHE* 3.6 22.4 - - + -
146H MET* 4.6 6.5 - - - -
151H ALA* 4.8 8.5 - - + +
154H LEU* 4.2 11.4 - - + -
155H VAL* 3.7 18.4 - - + -
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Residues in contact with VAL 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H VAL* 1.3 86.2 - - - +
8H TYR* 1.3 69.2 + - - +
11H GLY 3.3 13.0 - - - +
12H ILE* 3.8 12.3 - - + -
108H PRO* 3.3 27.8 - - + +
109H HIS* 4.4 3.1 - - + -
110H LEU* 4.1 7.0 - - + +
122H LEU 4.9 0.9 - - - +
123H PRO* 3.1 38.8 + - + +
142H PHE* 4.4 7.6 - - + -
145H ASP 5.7 1.6 + - - -
146H MET* 4.9 1.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il